Iron in PDB 7vw6: Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1

All present enzymatic activity of Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1:
1.17.1.9; 1.2.1.2;

The structure of Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1 also contains other interesting chemical elements:

Tungsten

(W)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1 (pdb code 7vw6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1, PDB code: 7vw6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in the Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:12.9 occ:1.00 FE1 A:SF41001 0.0 12.9 1.0 SG A:CYS219 2.3 8.6 1.0 S2 A:SF41001 2.3 12.9 1.0 S4 A:SF41001 2.3 12.9 1.0 S3 A:SF41001 2.3 12.9 1.0 FE4 A:SF41001 2.7 12.9 1.0 FE3 A:SF41001 2.7 12.9 1.0 FE2 A:SF41001 2.7 12.9 1.0 CB A:CYS219 3.2 8.6 1.0 N A:CYS219 3.8 8.6 1.0 S1 A:SF41001 3.9 12.9 1.0 CG2 A:VAL243 4.0 10.5 1.0 CA A:CYS219 4.1 8.6 1.0 CD1 A:LEU271 4.5 10.5 1.0 SG A:CYS216 4.7 9.8 1.0 SG A:CYS213 4.7 11.5 1.0 N A:LEU218 4.7 9.0 1.0 SG A:CYS266 4.8 9.0 1.0 N A:ASN217 4.9 9.9 1.0 C A:LEU218 5.0 9.0 1.0

Iron binding site 2 out of 20 in the Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:12.9 occ:1.00 FE2 A:SF41001 0.0 12.9 1.0 S1 A:SF41001 2.3 12.9 1.0 S3 A:SF41001 2.3 12.9 1.0 SG A:CYS216 2.3 9.8 1.0 S4 A:SF41001 2.3 12.9 1.0 FE4 A:SF41001 2.7 12.9 1.0 FE3 A:SF41001 2.7 12.9 1.0 FE1 A:SF41001 2.7 12.9 1.0 N A:CYS216 3.5 9.8 1.0 CB A:CYS216 3.6 9.8 1.0 S2 A:SF41001 3.9 12.9 1.0 CA A:CYS216 4.0 9.8 1.0 N A:ASN217 4.0 9.9 1.0 CD A:PRO267 4.1 10.5 1.0 N A:LEU218 4.2 9.0 1.0 C A:CYS216 4.3 9.8 1.0 N A:GLN215 4.5 10.9 1.0 C A:GLN215 4.6 10.9 1.0 SG A:CYS213 4.6 11.5 1.0 CG1 A:ILE214 4.6 10.9 1.0 SG A:CYS266 4.7 9.0 1.0 CB A:LEU218 4.7 9.0 1.0 SG A:CYS219 4.7 8.6 1.0 CG A:PRO267 4.8 10.5 1.0 N A:CYS219 4.8 8.6 1.0 CA A:GLN215 4.8 10.9 1.0 CA A:ASN217 4.9 9.9 1.0 N A:ILE214 5.0 10.9 1.0 C A:ASN217 5.0 9.9 1.0 CA A:LEU218 5.0 9.0 1.0

Iron binding site 3 out of 20 in the Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:12.9 occ:1.00 FE3 A:SF41001 0.0 12.9 1.0 SG A:CYS266 2.3 9.0 1.0 S4 A:SF41001 2.3 12.9 1.0 S2 A:SF41001 2.3 12.9 1.0 S1 A:SF41001 2.3 12.9 1.0 FE1 A:SF41001 2.7 12.9 1.0 FE4 A:SF41001 2.7 12.9 1.0 FE2 A:SF41001 2.7 12.9 1.0 CB A:CYS266 3.3 9.0 1.0 S3 A:SF41001 3.9 12.9 1.0 OG1 A:THR268 3.9 11.4 1.0 CA A:CYS266 3.9 9.0 1.0 CD A:PRO267 4.0 10.5 1.0 CB A:ALA270 4.2 10.8 1.0 CD1 A:LEU271 4.5 10.5 1.0 N A:PRO267 4.6 10.5 1.0 C A:CYS266 4.6 9.0 1.0 CG A:LEU271 4.6 10.5 1.0 SG A:CYS216 4.7 9.8 1.0 SG A:CYS219 4.8 8.6 1.0 SG A:CYS213 4.9 11.5 1.0

Iron binding site 4 out of 20 in the Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:12.9 occ:1.00 FE4 A:SF41001 0.0 12.9 1.0 SG A:CYS213 2.3 11.5 1.0 S1 A:SF41001 2.3 12.9 1.0 S3 A:SF41001 2.3 12.9 1.0 S2 A:SF41001 2.3 12.9 1.0 FE1 A:SF41001 2.7 12.9 1.0 FE2 A:SF41001 2.7 12.9 1.0 FE3 A:SF41001 2.7 12.9 1.0 CB A:CYS213 3.3 11.5 1.0 CA A:CYS213 3.7 11.5 1.0 S4 A:SF41001 3.9 12.9 1.0 N A:ILE214 4.0 10.9 1.0 N A:GLN215 4.0 10.9 1.0 CG2 A:VAL243 4.3 10.5 1.0 C A:CYS213 4.3 11.5 1.0 CA A:GLN215 4.5 10.9 1.0 CB A:ALA270 4.6 10.8 1.0 N A:CYS216 4.7 9.8 1.0 SG A:CYS219 4.8 8.6 1.0 OG1 A:THR268 4.8 11.4 1.0 SG A:CYS266 4.8 9.0 1.0 CD2 A:LEU210 4.9 12.4 1.0 SG A:CYS216 4.9 9.8 1.0 C A:ILE214 5.0 10.9 1.0 N A:CYS213 5.0 11.5 1.0

Iron binding site 5 out of 20 in the Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:11.8 occ:1.00 FE1 A:SF41002 0.0 11.8 1.0 SG A:CYS256 2.3 10.7 1.0 S3 A:SF41002 2.3 11.8 1.0 S4 A:SF41002 2.3 11.8 1.0 S2 A:SF41002 2.3 11.8 1.0 FE2 A:SF41002 2.7 11.8 1.0 FE4 A:SF41002 2.7 11.8 1.0 FE3 A:SF41002 2.7 11.8 1.0 CB A:CYS256 3.4 10.7 1.0 N A:ALA258 3.8 8.4 1.0 S1 A:SF41002 3.9 11.8 1.0 CA A:CYS256 3.9 10.7 1.0 N A:VAL257 4.0 9.1 1.0 C A:CYS256 4.3 10.7 1.0 CA A:ALA258 4.4 8.4 1.0 CE A:MET251 4.5 13.3 1.0 N A:CYS259 4.6 8.0 1.0 SG A:CYS262 4.8 8.3 1.0 CG2 A:VAL231 4.8 9.9 1.0 C A:VAL257 4.8 9.1 1.0 CG1 A:VAL231 4.8 9.9 1.0 CB A:VAL231 4.8 9.9 1.0 SG A:CYS259 4.9 8.0 1.0 SG A:CYS223 4.9 8.8 1.0 CE A:MET206 4.9 12.8 1.0 C A:ALA258 5.0 8.4 1.0

Iron binding site 6 out of 20 in the Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:11.8 occ:1.00 FE2 A:SF41002 0.0 11.8 1.0 SG A:CYS259 2.3 8.0 1.0 S4 A:SF41002 2.3 11.8 1.0 S3 A:SF41002 2.3 11.8 1.0 S1 A:SF41002 2.3 11.8 1.0 FE1 A:SF41002 2.7 11.8 1.0 FE4 A:SF41002 2.7 11.8 1.0 FE3 A:SF41002 2.7 11.8 1.0 N A:CYS259 3.5 8.0 1.0 CB A:CYS259 3.5 8.0 1.0 N A:GLY260 3.7 8.3 1.0 S2 A:SF41002 3.9 11.8 1.0 ND2 A:ASN229 3.9 9.3 1.0 CA A:CYS259 3.9 8.0 1.0 C A:CYS259 4.2 8.0 1.0 N A:GLU261 4.2 8.3 1.0 C A:ALA258 4.5 8.4 1.0 N A:ALA258 4.6 8.4 1.0 CA A:GLY260 4.6 8.3 1.0 SG A:CYS223 4.7 8.8 1.0 SG A:CYS262 4.7 8.3 1.0 SG A:CYS256 4.8 10.7 1.0 CA A:ALA258 4.8 8.4 1.0 CB A:GLU261 4.9 8.3 1.0 CG2 A:VAL257 4.9 9.1 1.0 C A:GLY260 4.9 8.3 1.0 CG A:ASN229 4.9 9.3 1.0 N A:CYS262 5.0 8.3 1.0

Iron binding site 7 out of 20 in the Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:11.8 occ:1.00 FE3 A:SF41002 0.0 11.8 1.0 SG A:CYS262 2.3 8.3 1.0 S1 A:SF41002 2.3 11.8 1.0 S4 A:SF41002 2.3 11.8 1.0 S2 A:SF41002 2.3 11.8 1.0 FE4 A:SF41002 2.7 11.8 1.0 FE1 A:SF41002 2.7 11.8 1.0 FE2 A:SF41002 2.7 11.8 1.0 CB A:CYS262 3.4 8.3 1.0 S3 A:SF41002 3.9 11.8 1.0 N A:CYS262 4.0 8.3 1.0 CD1 A:ILE232 4.3 9.5 1.0 CA A:CYS262 4.3 8.3 1.0 CE A:MET251 4.4 13.3 1.0 SG A:CYS223 4.6 8.8 1.0 N A:GLU261 4.7 8.3 1.0 SG A:CYS259 4.7 8.0 1.0 SG A:CYS256 4.7 10.7 1.0 N A:GLY260 4.7 8.3 1.0 CB A:CYS223 4.9 8.8 1.0 CA A:GLY260 5.0 8.3 1.0 CG1 A:ILE232 5.0 9.5 1.0 C A:GLY260 5.0 8.3 1.0

Iron binding site 8 out of 20 in the Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:11.8 occ:1.00 FE4 A:SF41002 0.0 11.8 1.0 SG A:CYS223 2.3 8.8 1.0 S1 A:SF41002 2.3 11.8 1.0 S2 A:SF41002 2.3 11.8 1.0 S3 A:SF41002 2.3 11.8 1.0 FE3 A:SF41002 2.7 11.8 1.0 FE1 A:SF41002 2.7 11.8 1.0 FE2 A:SF41002 2.7 11.8 1.0 CB A:CYS223 3.4 8.8 1.0 CB A:VAL231 3.9 9.9 1.0 S4 A:SF41002 3.9 11.8 1.0 CG2 A:VAL231 4.1 9.9 1.0 CA A:CYS223 4.2 8.8 1.0 CB A:ASN229 4.4 9.3 1.0 CG1 A:ILE232 4.6 9.5 1.0 CG1 A:VAL231 4.6 9.9 1.0 ND2 A:ASN229 4.6 9.3 1.0 CD1 A:ILE232 4.7 9.5 1.0 SG A:CYS259 4.7 8.0 1.0 SG A:CYS262 4.8 8.3 1.0 SG A:CYS256 4.9 10.7 1.0 N A:VAL231 4.9 9.9 1.0 CA A:VAL231 4.9 9.9 1.0

Iron binding site 9 out of 20 in the Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1003 b:15.5 occ:1.00 FE1 A:FES1003 0.0 15.5 1.0 S1 A:FES1003 2.2 15.5 1.0 S2 A:FES1003 2.2 15.5 1.0 SG A:CYS118 2.3 14.8 1.0 SG A:CYS132 2.3 16.5 1.0 FE2 A:FES1003 3.1 15.5 1.0 CB A:CYS132 3.1 16.5 1.0 CB A:CYS118 3.3 14.8 1.0 N A:CYS132 4.1 16.5 1.0 CA A:CYS132 4.2 16.5 1.0 N A:CYS118 4.3 14.8 1.0 SG A:CYS102 4.4 11.7 1.0 CA A:CYS118 4.4 14.8 1.0 CB A:ALA130 4.4 16.7 1.0 CA A:GLY113 4.5 11.6 1.0 CB A:HIS103 4.6 13.8 1.0 C A:CYS132 4.9 16.5 1.0 SG A:CYS115 5.0 10.9 1.0

Iron binding site 10 out of 20 in the Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of Formate Dehydrogenase 1 From Methylorubrum Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1003 b:15.5 occ:1.00 FE2 A:FES1003 0.0 15.5 1.0 S2 A:FES1003 2.2 15.5 1.0 S1 A:FES1003 2.2 15.5 1.0 SG A:CYS115 2.3 10.9 1.0 SG A:CYS102 2.3 11.7 1.0 FE1 A:FES1003 3.1 15.5 1.0 CB A:CYS102 3.3 11.7 1.0 CB A:CYS115 3.3 10.9 1.0 N A:CYS102 3.4 11.7 1.0 N A:CYS115 3.5 10.9 1.0 N A:ARG116 3.7 12.1 1.0 CA A:CYS115 3.8 10.9 1.0 CA A:CYS102 3.8 11.7 1.0 C A:CYS115 4.1 10.9 1.0 N A:HIS103 4.2 13.8 1.0 C A:CYS102 4.3 11.7 1.0 N A:ALA117 4.3 14.0 1.0 N A:ASN114 4.3 10.4 1.0 N A:LEU101 4.4 12.8 1.0 C A:LEU101 4.5 12.8 1.0 SG A:CYS132 4.6 16.5 1.0 C A:ASN114 4.6 10.4 1.0 CA A:GLY113 4.6 11.6 1.0 C A:GLY113 4.7 11.6 1.0 CA A:ARG116 4.7 12.1 1.0 CA A:LEU101 4.9 12.8 1.0 SG A:CYS118 5.0 14.8 1.0

T.Yoshikawa, F.Makino, T.Miyata, Y.Suzuki, H.Tanaka, K.Namba, K.Kano, K.Sowa, Y.Kitazumi, O.Shirai. Multiple Electron Transfer Pathways of Tungsten-Containing Formate Dehydrogenase in Direct Electron Transfer-Type Bioelectrocatalysis. Chem.Commun.(Camb.) V. 58 6478 2022.
ISSN: ESSN 1364-548X
PubMed: 35535582
DOI: 10.1039/D2CC01541B